Mercurial > repos > devteam > fastq_to_fasta

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit fd099d17eceaa319fbfe429f4725328d88b18c9f
author iuc
date Thu, 10 Aug 2023 06:53:23 +0000
parents 8979c288aefb
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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1 <?xml version="1.0"?>
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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2 <macros>
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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3 <token name="@CATS@">
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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4 #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'):
3
02a5f43cd5d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit 3953b65f6b1c0336e9cadbe0792a5d3b14b5643a
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5 gunzip -c -f '$input' |
2
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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6 #elif $input.is_of_type('fastqsanger.bz2', 'fastqsolexa.bz2', 'fastqillumina.bz2'):
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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7 bzcat -f '$input' |
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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8 #else:
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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9 cat '$input' |
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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10 #end if
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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11 </token>
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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12 <token name="@FQQUAL@">
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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13 <![CDATA[
6
77b41c89d856 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit fd099d17eceaa319fbfe429f4725328d88b18c9f
iuc
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14 #if $input.is_of_type('fastqsanger', 'fastqsanger.gz', 'fastqsanger.bz2'):
2
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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15 -Q 33
6
77b41c89d856 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit fd099d17eceaa319fbfe429f4725328d88b18c9f
iuc
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16 #elif $input.is_of_type('fastqsolexa', 'fastqsolexa.gz', 'fastqsolexa.bz2', 'fastqillumina', 'fastqillumina.gz', 'fastqillumina.bz2'):
2
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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17 -Q 64
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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18 #end if
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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19 ]]>
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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20 </token>
6
77b41c89d856 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit fd099d17eceaa319fbfe429f4725328d88b18c9f
iuc
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21 <token name="@GZIP@">
77b41c89d856 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit fd099d17eceaa319fbfe429f4725328d88b18c9f
iuc
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22 <![CDATA[
77b41c89d856 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit fd099d17eceaa319fbfe429f4725328d88b18c9f
iuc
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23 #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'):
77b41c89d856 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit fd099d17eceaa319fbfe429f4725328d88b18c9f
iuc
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24 | gzip -c
77b41c89d856 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit fd099d17eceaa319fbfe429f4725328d88b18c9f
iuc
parents: 5
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25 #elif $input.is_of_type('fastqsanger.bz2', 'fastqsolexa.bz2', 'fastqillumina.bz2'):
77b41c89d856 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit fd099d17eceaa319fbfe429f4725328d88b18c9f
iuc
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26 | bzip2 -c
77b41c89d856 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit fd099d17eceaa319fbfe429f4725328d88b18c9f
iuc
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27 #end if
77b41c89d856 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit fd099d17eceaa319fbfe429f4725328d88b18c9f
iuc
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28 ]]>
77b41c89d856 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit fd099d17eceaa319fbfe429f4725328d88b18c9f
iuc
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29 </token>
2
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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30 <xml name="requirements">
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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31 <requirements>
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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32 <requirement type="package" version="@VERSION@">fastx_toolkit</requirement>
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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33 <yield />
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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34 </requirements>
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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35 </xml>
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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36 <token name="@VERSION@">0.0.14</token>
6
77b41c89d856 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit fd099d17eceaa319fbfe429f4725328d88b18c9f
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37 <token name="@VERSION_SUFFIX@">2</token>
2
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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38 <token name="@SANGER@">fastqsanger,fastqsanger.gz,fastqsanger.bz2</token>
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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39 <token name="@SOLEXA@">fastqsolexa,fastqsolexa.gz,fastqsolexa.bz2</token>
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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40 <token name="@ILLUMINA@">fastqillumina,fastqillumina.gz,fastqillumina.bz2</token>
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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41 <token name="@FASTQS@">@SANGER@,@SOLEXA@,@ILLUMINA@</token>
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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42 <token name="@FASTAS@">fasta,fasta.gz</token>
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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43 <xml name="citations">
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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44 <citations>
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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45 <citation type="bibtex">
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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46 @UNPUBLISHED{agordon,
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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47 author = "Assaf Gordon",
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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48 title = "FASTQ/A short-reads pre-processing tools",
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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49 year = "2010",
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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50 note = "http://hannonlab.cshl.edu/fastx_toolkit/",
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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51 url = "http://hannonlab.cshl.edu/fastx_toolkit/"}
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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52 </citation>
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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53 </citations>
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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54 </xml>
6
77b41c89d856 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit fd099d17eceaa319fbfe429f4725328d88b18c9f
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55 <xml name="fasta_input">
77b41c89d856 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit fd099d17eceaa319fbfe429f4725328d88b18c9f
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56 <param name="input" type="data" format="@FASTAS@" label="Input FASTA file" />
77b41c89d856 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit fd099d17eceaa319fbfe429f4725328d88b18c9f
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57 </xml>
2
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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58 <xml name="fastq_input">
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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59 <param name="input" type="data" format="@FASTQS@" label="Input FASTQ file" />
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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60 </xml>
6
77b41c89d856 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit fd099d17eceaa319fbfe429f4725328d88b18c9f
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61 <xml name="fastx_input">
77b41c89d856 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit fd099d17eceaa319fbfe429f4725328d88b18c9f
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62 <param name="input" type="data" format="@FASTAS@,@FASTQS@" label="Input file in FASTA or FASTQ format" />
77b41c89d856 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit fd099d17eceaa319fbfe429f4725328d88b18c9f
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63 </xml>
2
ce309f4ff17f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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64 </macros>